The polymerase chain reaction (PCR) has rapidly become indispensable in both basic research and clinical diagnostics. Rapid cycle PCR is a technique that reduces cycle times by an order of magnitude and improves product specificity. PCR can be continuously monitored with fluorescent intercalating dyes, but intercalation is not sequence specific. Our objective is to develop optical methods and instrumentation for continuously monitoring specific PCR product formation during rapid temperature cycling. If a probe hybridizes to single stranded product during PCR, fluorescence techniques can be used to continuously monitor product formation. Various probe/fluorophore configurations will be synthesized and their sensitivity in the PCR determined. A simple, prototype instrument with xenon flash illumination of a capillary tube will be developed for continuous monitoring. The feasibility of monitoring multiple samples will be assessed in a modified flow cytometer with a rotating carousel. Homogenous monitoring in a sealed system reduces potential contamination and continuous monitoring greatly simplifies quantitative PCR. An instrument that amplifies and provides quantitative results in less than 15 min with the specificity of an external probe will have many applications.